I have been using a set of scripts to preprocess fMRI data for a study involving irritability tasks. These scripts have worked without issues for a long time. However, after updating to AFNI version AFNI_24.3.05 ('Elagabalus'), I've encountered a problem. While the preprocessing completes successfully and the QC files are generated, the "sum of regressors" and "regressors of interest" plots are missing from the output.
No changes have been made to the scripts themselves. Has anyone else encountered this problem or have suggestions on how to resolve it?
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I was able to fix the matplotlib with numpy 2.2.2 issue, and some of the missing sections load now. However, there are still some missing sections, some that weren't previously missing that are now. Here is the updated output from the afni_system_check.py -check_all command:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 6.8.0-52-generic
version: #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 19:18:46 UTC 2
distribution: ubuntu 22.04 Jammy Jellyfish
number of CPUs: 40
apparent login shell: tcsh
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/afni
afni version : Precompiled binary linux_ubuntu_16_64: Oct 26 2024
: AFNI_24.3.05 'Elagabalus'
AFNI_version.txt : AFNI_24.3.05, linux_ubuntu_16_64, Oct 26 2024, official
which python : /usr/bin/python
python version : 3.10.12
which R : /usr/bin/R
R version : R version 4.4.3 (x86_64-pc-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/usr/local/afni/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.10)
python2 : 0
python3 : 1 (/usr/bin/python3.10)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
tcsh version : 6.21.00
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /usr/lib/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
matplotlib version : 3.5.1
++ module loaded: flask
module file : /usr/lib/python3/dist-packages/flask/__init__.py
flask version : 2.0.1
++ module loaded: flask_cors
module file : /usr/lib/python3/dist-packages/flask_cors/__init__.py
flask_cors version : 3.0.9
-------------------------------- env vars --------------------------------
PATH = /usr/local/afni:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni:/usr/local/afni
PYTHONPATH =
R_LIBS = /usr/local/R_libs
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
CC =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 1 modifications across 2 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/afni
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.13 (amd64)
have Ubuntu system: ubuntu 22.04 Jammy Jellyfish
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Oct 26 2024
========================= summary, please fix: =========================
* dot file test : want 1 modifications across 2 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.